Spinal cord data#

Morphometry#

Code imports#

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd

# Import custom tools
from tools.data import Data
from tools.plot import Plot

Download data#

data_type = 'spine'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)
--2022-08-04 22:09:19--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20210610/spinalcord_results.zip
Resolving github.com (github.com)... 140.82.112.3
Connecting to github.com (github.com)|140.82.112.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220804%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220804T220919Z&X-Amz-Expires=300&X-Amz-Signature=3dc4af92c476d7730f0d507e8ac83a8a1730db151d9824279459fa8550531eb9&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream [following]
--2022-08-04 22:09:19--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220804%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220804T220919Z&X-Amz-Expires=300&X-Amz-Signature=3dc4af92c476d7730f0d507e8ac83a8a1730db151d9824279459fa8550531eb9&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.111.133, 185.199.110.133, 185.199.109.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 19324 (19K) [application/octet-stream]
Saving to: ‘spinalcord_results.zip’

     0K .......... ........                                   100% 7.78M=0.002s

2022-08-04 22:09:19 (7.78 MB/s) - ‘spinalcord_results.zip’ saved [19324/19324]
Archive:  spinalcord_results.zip
  inflating: data/spine/DWI_RD.csv   
  inflating: data/spine/DWI_FA.csv   
  inflating: data/spine/csa-SC_T2w.csv  
  inflating: data/spine/DWI_MD.csv   
  inflating: data/spine/MTR.csv      
  inflating: data/spine/MTsat.csv    
  inflating: data/spine/csa-GM_T2s.csv  
  inflating: data/spine/csa-SC_T1w.csv  
  inflating: data/spine/._csa-SC_T1w.csv  
  inflating: data/spine/T1.csv       

Load data plot it#

dataset.num_sessions
dataset.load()

fig_spine = Plot(dataset, plot_name = 'spine-wm')

fig_spine.title = 'WM spinal cord morphometry'

White matter#

# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', fig_id = 'spine-csa-wm')

Grey matter#

fig_spine = Plot(dataset, plot_name = 'spine-gm')

fig_spine.title = 'GM spinal cord morphometry'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', fig_id = 'spine-csa-gm')

Quantitative MRI#

White matter#

data_type = 'qmri'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)
Archive:  spinalcord_results.zip
  inflating: data/qmri/DWI_RD.csv    
  inflating: data/qmri/DWI_FA.csv    
  inflating: data/qmri/csa-SC_T2w.csv  
  inflating: data/qmri/DWI_MD.csv    
  inflating: data/qmri/MTR.csv       
  inflating: data/qmri/MTsat.csv     
  inflating: data/qmri/csa-GM_T2s.csv  
  inflating: data/qmri/csa-SC_T1w.csv  
  inflating: data/qmri/._csa-SC_T1w.csv  
  inflating: data/qmri/T1.csv        
--2022-08-04 22:09:20--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20210610/spinalcord_results.zip
Resolving github.com (github.com)... 140.82.112.3
Connecting to github.com (github.com)|140.82.112.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220804%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220804T220919Z&X-Amz-Expires=300&X-Amz-Signature=3dc4af92c476d7730f0d507e8ac83a8a1730db151d9824279459fa8550531eb9&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream [following]
--2022-08-04 22:09:20--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220804%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220804T220919Z&X-Amz-Expires=300&X-Amz-Signature=3dc4af92c476d7730f0d507e8ac83a8a1730db151d9824279459fa8550531eb9&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.111.133, 185.199.110.133, 185.199.109.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 19324 (19K) [application/octet-stream]
Saving to: ‘spinalcord_results.zip’

     0K .......... ........                                   100% 30.5M=0.001s

2022-08-04 22:09:20 (30.5 MB/s) - ‘spinalcord_results.zip’ saved [19324/19324]
dataset.load()
fig_spine = Plot(dataset, plot_name = 'spine-2')
fig_spine.title = 'Spinal cord qMRI measures'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', fig_id = 'spine-qmri-wm')